After danger is safely dealt with in The Crystal Empire, the ponies race back to Ponyville to discover that the eventual time has now passed for something new. A new danger creeps out of the Everfree Forest, and the Mane 6 race to find out what will happen to their beloved town and home, but end up losing Fluttershy. She herself battles to find out what she will do in this new era, theorized by the Mane 6, and what it is in reality.